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Open data
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Basic information
Entry | Database: PDB / ID: 7x5u | ||||||
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Title | Crystal structure of AtHPPD-diketonitrile complex | ||||||
![]() | 4-hydroxyphenylpyruvate dioxygenase | ||||||
![]() | OXIDOREDUCTASE / inhibitor / complex | ||||||
Function / homology | ![]() 4-hydroxyphenylpyruvate dioxygenase / 4-hydroxyphenylpyruvate dioxygenase activity / tyrosine catabolic process / L-phenylalanine catabolic process / iron ion binding / Golgi membrane / endoplasmic reticulum membrane / identical protein binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lin, H.-Y. / Dong, J. / Yang, G.-F. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural insights of 4-Hydrophenylpyruvate dioxygenase inhibition by structurally diverse small molecules Authors: Dong, J. / Dong, J. / Yu, X.H. / Yan, Y.C. / Nan, J.X. / He, B. / Ye, B.Q. / Yang, W.C. / Lin, H.Y. / Yang, G.F. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 97.3 KB | Display | ![]() |
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PDB format | ![]() | 69.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 820.1 KB | Display | ![]() |
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Full document | ![]() | 825.4 KB | Display | |
Data in XML | ![]() | 19 KB | Display | |
Data in CIF | ![]() | 27.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7cqrC ![]() 7cqsSC ![]() 7x5rC ![]() 7x5sC ![]() 7x5wC ![]() 7x5xC ![]() 7x6mC ![]() 7x6nC ![]() 7x7lC ![]() 7x8dC ![]() 7x8eC ![]() 7xntC S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 45952.727 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Production host: ![]() ![]() References: UniProt: P93836, 4-hydroxyphenylpyruvate dioxygenase |
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#2: Chemical | ChemComp-CO / |
#3: Chemical | ChemComp-9R6 / ( |
#4: Chemical | ChemComp-MPD / ( |
#5: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.41 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.1M Tris/Bicine pH 8.5, 15% (v/v) MPD, 15% (w/v) PEG 1000, 15% (w/v) PEG 3350, 0.03M NaBr, 0.03M NaF, 0.03M NaI |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 22, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9875 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→30 Å / Num. obs: 43138 / % possible obs: 84.1 % / Redundancy: 2.4 % / CC1/2: 0.996 / Rmerge(I) obs: 0.045 / Net I/σ(I): 18.7 |
Reflection shell | Resolution: 1.6→1.63 Å / Rmerge(I) obs: 0.312 / Num. unique obs: 1931 / CC1/2: 0.88 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7CQS Resolution: 1.6→28.434 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 23.82 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→28.434 Å
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Refine LS restraints |
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LS refinement shell |
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